/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
public class ShiftList\r
{\r
- public Vector shifts;\r
+ public Vector shifts;\r
public ShiftList()\r
{\r
shifts = new Vector();\r
public void addShift(int pos, int shift)\r
{\r
int sidx = 0;\r
- int[] rshift=null;\r
- while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)\r
+ int[] rshift = null;\r
+ while (sidx < shifts.size() &&\r
+ (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)\r
+ {\r
sidx++;\r
- if (sidx==shifts.size())\r
- shifts.insertElementAt(new int[] { pos, shift}, sidx);\r
+ }\r
+ if (sidx == shifts.size())\r
+ {\r
+ shifts.insertElementAt(new int[]\r
+ {pos, shift}, sidx);\r
+ }\r
else\r
- rshift[1]+=shift;\r
+ {\r
+ rshift[1] += shift;\r
+ }\r
}\r
\r
/**\r
*/\r
public int shift(int pos)\r
{\r
- if (shifts.size()==0)\r
+ if (shifts.size() == 0)\r
+ {\r
return pos;\r
- int shifted=pos;\r
- int sidx=0;\r
+ }\r
+ int shifted = pos;\r
+ int sidx = 0;\r
int rshift[];\r
- while (sidx<shifts.size()\r
+ while (sidx < shifts.size()\r
&&\r
- (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {\r
+ (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)\r
+ {\r
shifted += rshift[1];\r
}\r
return shifted;\r
{\r
shifts.removeAllElements();\r
}\r
+\r
/**\r
* invert the shifts\r
* @return ShiftList with inverse shift operations\r
*/\r
- public ShiftList getInverse() {\r
- ShiftList inverse=new ShiftList();\r
- if (shifts!=null) {\r
- for (int i=0,j=shifts.size(); i<j; i++) {\r
- int[] sh=(int[]) shifts.elementAt(i);\r
- if (sh!=null)\r
- inverse.shifts.addElement(new int[] {sh[0], -sh[1]});\r
+ public ShiftList getInverse()\r
+ {\r
+ ShiftList inverse = new ShiftList();\r
+ if (shifts != null)\r
+ {\r
+ for (int i = 0, j = shifts.size(); i < j; i++)\r
+ {\r
+ int[] sh = (int[]) shifts.elementAt(i);\r
+ if (sh != null)\r
+ {\r
+ inverse.shifts.addElement(new int[]\r
+ {sh[0], -sh[1]});\r
+ }\r
}\r
}\r
return inverse;\r
* @param gapMap\r
* @return shifts from map index to mapped position\r
*/\r
- public static ShiftList parseMap(int[] gapMap) {\r
+ public static ShiftList parseMap(int[] gapMap)\r
+ {\r
ShiftList shiftList = null;\r
- if (gapMap!=null && gapMap.length>0) {\r
- shiftList=new ShiftList();\r
- for (int i=0,p=0; i<gapMap.length; p++,i++) {\r
- if (p!=gapMap[i]) {\r
- shiftList.addShift(p, gapMap[i]-p);\r
- p=gapMap[i];\r
+ if (gapMap != null && gapMap.length > 0)\r
+ {\r
+ shiftList = new ShiftList();\r
+ for (int i = 0, p = 0; i < gapMap.length; p++, i++)\r
+ {\r
+ if (p != gapMap[i])\r
+ {\r
+ shiftList.addShift(p, gapMap[i] - p);\r
+ p = gapMap[i];\r
}\r
}\r
}\r